Wuchereria bancrofti (Wb) is the primary causative agent of lymphatic filariasis (LF), a disfiguring and debilitating vector-borne disease estimated t affect 120 million people in 83 countries. Our studies in Papua New Guinea have shown that it is possible to reduce the prevalence of Wb in human and mosquito infections by mass drug administration (MDA), however without continued drug pressure, transmission has shown signs of recovering to pre-MDA levels. These results suggest that drugs used to kill Wb are not completely effective. This exposes a significant gap in strategies used to monitor LF elimination programs - to date conventional population genetic tools have not been available for Wb. It follows then that genetic diversity of Wb has not been measured, there is no information regarding its population size, its potential for variation, nor its capacity to evade or recover frm MDA. Through recent successful completion of the Wb mitochondrial (mt) genome sequence, we have begun to address the limited ability to monitor Wb elimination through population genetic strategies. Here, we describe approaches for analyzing complete mt genome sequence through next-generation sequencing technology allowing us to provide in-depth analysis of sequence diversity within multiple individual samples. Through the following Specific Aims our proposal provides innovative, new quantitative strategies to monitor the population impact of LF elimination. Aim 1: Define the diversity of Wb infections within individuals and populations in areas anticipating clinical trials of anti-filarial drugs. We will amplify three overlapping segmens of the entire Wb mt genome from individual patients and generate sequencing libraries barcoded with primers containing unique 6-nucleotide identifiers. We will then pool libraries and sequence them on one lane of HiSeq 2000. This approach generates coverage necessary to account for inherent variations to pooling, to identify true polymorphism, and identify multiple parasite haplotypes. Resulting data can be used to estimate previously unknown life history parameters for Wb, (e.g. genetic diversity, effective number of infections, effective reproductive rate (Ro), and migration rates). The resulting database will also enable pre- and post-MDA treatment comparisons to monitor elimination programs and track emergence of drug resistance strains. Aim 2: Evaluate the response of individual infections to anti-filarial drugs through seria assessment of patient samples following treatment. Our collaboration with Dr. James Kazura will provide samples from Wb-infected patients collected at pre-treatment and 14 day, 1-, 3-, 6- and 12-month post-treatment time points. By sequencing patient infections during treatment we can collect additional data on treatment effectiveness beyond just parasite load, providing insight into the interactions between genetic diversity, parasitemia, and drug efficacy. As these population-level studies address an important gap in Wb epidemiology and elimination programs, our results have potential to strengthen design of future MDA efforts beyond PNG.